@genome-spy/core 0.73.0 → 0.75.0

package/dist/bundle/index-CRaQAuki.js

@@ -1,326 +0,0 @@
-const _ = /%([0-9A-Fa-f]{2})/g, b = /^\s*##\s*(\S+)\s*(.*)/, C = /\r?\n$/, p = /\s+/, m = /\D/g;
-function f(n) {
-  return n.includes("%") ? n.replaceAll(_, (e, r) => String.fromCharCode(parseInt(r, 16))) : n;
-}
-function v(n) {
-  if (!n.length || n === ".")
-    return {};
-  const e = {};
-  let r = n;
-  r.endsWith(`
-`) && (r = r.slice(0, r.endsWith(`\r
-`) ? -2 : -1));
-  for (const t of r.split(";")) {
-    const i = t.indexOf("=");
-    if (i === -1)
-      continue;
-    const s = t.slice(i + 1);
-    if (!s.length)
-      continue;
-    const o = t.slice(0, i).trim();
-    let c = e[o];
-    c || (c = [], e[o] = c);
-    for (const l of s.split(","))
-      c.push(f(l.trim()));
-  }
-  return e;
-}
-function F(n) {
-  if (!n.length || n === ".")
-    return {};
-  const e = {};
-  let r = n;
-  r.endsWith(`
-`) && (r = r.slice(0, r.endsWith(`\r
-`) ? -2 : -1));
-  for (const t of r.split(";")) {
-    const i = t.indexOf("=");
-    if (i === -1)
-      continue;
-    const s = t.slice(i + 1);
-    if (!s.length)
-      continue;
-    const o = t.slice(0, i).trim();
-    let c = e[o];
-    c || (c = [], e[o] = c);
-    for (const l of s.split(","))
-      c.push(l.trim());
-  }
-  return e;
-}
-function y(n) {
-  return d(n.split("	"));
-}
-function a(n) {
-  return n === "." || n === "" || n === void 0 ? null : n;
-}
-function d(n) {
-  const e = a(n[0]), r = a(n[1]), t = a(n[2]), i = a(n[3]), s = a(n[4]), o = a(n[5]), c = a(n[6]), l = a(n[7]), u = a(n[8]);
-  return {
-    seq_id: e ? f(e) : null,
-    source: r ? f(r) : null,
-    type: t ? f(t) : null,
-    start: i === null ? null : parseInt(i, 10),
-    end: s === null ? null : parseInt(s, 10),
-    score: o === null ? null : parseFloat(o),
-    strand: c,
-    phase: l,
-    attributes: u === null ? null : v(u)
-  };
-}
-function R(n) {
-  const e = a(n[0]), r = a(n[1]), t = a(n[2]), i = a(n[3]), s = a(n[4]), o = a(n[5]), c = a(n[6]), l = a(n[7]), u = a(n[8]);
-  return {
-    seq_id: e,
-    source: r,
-    type: t,
-    start: i === null ? null : parseInt(i, 10),
-    end: s === null ? null : parseInt(s, 10),
-    score: o === null ? null : parseFloat(o),
-    strand: c,
-    phase: l,
-    attributes: u === null ? null : F(u)
-  };
-}
-function g(n) {
-  const e = b.exec(n);
-  if (!e)
-    return null;
-  const [, r] = e;
-  let [, , t] = e;
-  const i = { directive: r };
-  if (t.length && (t = t.replace(C, ""), i.value = t), r === "sequence-region") {
-    const s = t.split(p, 3);
-    return {
-      ...i,
-      seq_id: s[0],
-      start: s[1]?.replaceAll(m, ""),
-      end: s[2]?.replaceAll(m, "")
-    };
-  } else if (r === "genome-build") {
-    const [s, o] = t.split(p, 2);
-    return {
-      ...i,
-      source: s,
-      buildName: o
-    };
-  }
-  return i;
-}
-const k = /^\s*[^#\s>]/, I = /^\s*(#+)(.*)/, L = /^\s*$/, D = /^\s*>/, A = /\r?\n?$/g;
-class h {
-  featureCallback;
-  endCallback;
-  commentCallback;
-  errorCallback;
-  disableDerivesFromReferences;
-  directiveCallback;
-  bufferSize;
-  eof = !1;
-  lineNumber = 0;
-  // features that we have to keep on hand for now because they
-  // might be referenced by something else
-  _underConstructionTopLevel = [];
-  // index of the above by ID
-  _underConstructionById = {};
-  _completedReferences = {};
-  // features that reference something we have not seen yet
-  // structured as:
-  // {  'some_id' : {
-  //     'Parent' : [ orphans that have a Parent attr referencing it ],
-  //     'Derives_from' : [ orphans that have a Derives_from attr referencing it ],
-  //    }
-  // }
-  _underConstructionOrphans = {};
-  constructor(e) {
-    const r = () => {
-    };
-    this.featureCallback = e.featureCallback || r, this.endCallback = e.endCallback || r, this.commentCallback = e.commentCallback || r, this.errorCallback = e.errorCallback || r, this.directiveCallback = e.directiveCallback || r, this.disableDerivesFromReferences = e.disableDerivesFromReferences || !1, this.bufferSize = e.bufferSize === void 0 ? 1 / 0 : e.bufferSize;
-  }
-  addLine(e) {
-    if (this.eof)
-      return;
-    if (this.lineNumber += 1, k.test(e)) {
-      this._bufferLine(e);
-      return;
-    }
-    const r = I.exec(e);
-    if (r) {
-      const [, t] = r;
-      let [, , i] = r;
-      if (t.length === 3)
-        this._emitAllUnderConstructionFeatures();
-      else if (t.length === 2) {
-        const s = g(e);
-        s && (s.directive === "FASTA" ? (this._emitAllUnderConstructionFeatures(), this.eof = !0) : this._emitItem(s));
-      } else
-        this._emitItem({ comment: i.trimStart() });
-    } else if (!L.test(e)) if (D.test(e))
-      this._emitAllUnderConstructionFeatures(), this.eof = !0;
-    else {
-      const t = e.replaceAll(A, "");
-      throw new Error(`GFF3 parse error.  Cannot parse '${t}'.`);
-    }
-  }
-  addParsedFeatureLine(e) {
-    this.eof || (this.lineNumber += 1, this._bufferParsedLine(e));
-  }
-  finish() {
-    this._emitAllUnderConstructionFeatures(), this.endCallback();
-  }
-  _emitItem(e) {
-    Array.isArray(e) ? this.featureCallback(e) : "directive" in e ? this.directiveCallback(e) : "comment" in e && this.commentCallback(e);
-  }
-  _enforceBufferSizeLimit(e = 0) {
-    const r = (t) => {
-      t && Array.isArray(t) && t[0].attributes?.ID?.[0] && (t[0].attributes.ID.forEach((s) => {
-        delete this._underConstructionById[s], delete this._completedReferences[s];
-      }), t.forEach((s) => {
-        s.child_features && s.child_features.forEach((o) => {
-          r(o);
-        }), s.derived_features && s.derived_features.forEach((o) => {
-          r(o);
-        });
-      }));
-    };
-    for (; this._underConstructionTopLevel.length + e > this.bufferSize; ) {
-      const t = this._underConstructionTopLevel.shift();
-      t && (this._emitItem(t), r(t));
-    }
-  }
-  /**
-   * return all under-construction features, called when we know
-   * there will be no additional data to attach to them
-   */
-  _emitAllUnderConstructionFeatures() {
-    this._underConstructionTopLevel.forEach(this._emitItem.bind(this)), this._underConstructionTopLevel = [], this._underConstructionById = {}, this._completedReferences = {};
-    const e = Object.keys(this._underConstructionOrphans);
-    if (e.length)
-      throw new Error(`some features reference other features that do not exist in the file (or in the same '###' scope). ${e.join(",")}`);
-  }
-  _bufferLine(e) {
-    this._bufferParsedLine(y(e));
-  }
-  _bufferParsedLine(e) {
-    const r = e;
-    r.child_features = [], r.derived_features = [];
-    const t = r.attributes?.ID || [], i = r.attributes?.Parent || [], s = this.disableDerivesFromReferences ? [] : r.attributes?.Derives_from || [];
-    if (!t.length && !i.length && !s.length) {
-      this._emitItem([r]);
-      return;
-    }
-    let o;
-    t.forEach((c) => {
-      const l = this._underConstructionById[c];
-      l ? (l[l.length - 1].type !== r.type && this._parseError(`multi-line feature "${c}" has inconsistent types: "${r.type}", "${l[l.length - 1].type}"`), l.push(r), o = l) : (o = [r], this._enforceBufferSizeLimit(1), !i.length && !s.length && this._underConstructionTopLevel.push(o), this._underConstructionById[c] = o, this._resolveReferencesTo(o, c));
-    }), this._resolveReferencesFrom(
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-      o || [r],
-      { Parent: i, Derives_from: s },
-      t
-    );
-  }
-  _resolveReferencesTo(e, r) {
-    const t = this._underConstructionOrphans[r];
-    if (t) {
-      for (const i of e)
-        i.child_features.push(...t.Parent), i.derived_features.push(...t.Derives_from);
-      delete this._underConstructionOrphans[r];
-    }
-  }
-  _parseError(e) {
-    this.eof = !0, this.errorCallback(`${this.lineNumber}: ${e}`);
-  }
-  _resolveReferencesFrom(e, r, t) {
-    for (const i of r.Parent) {
-      const s = this._underConstructionById[i];
-      if (s) {
-        let o = !1;
-        for (const c of t) {
-          const l = `Parent,${i}`, u = this._completedReferences[c] || (this._completedReferences[c] = {});
-          u[l] && (o = !0), u[l] = !0;
-        }
-        if (!o)
-          for (const c of s)
-            c.child_features.push(e);
-      } else {
-        let o = this._underConstructionOrphans[i];
-        o || (o = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[i] = o), o.Parent.push(e);
-      }
-    }
-    for (const i of r.Derives_from) {
-      const s = this._underConstructionById[i];
-      if (s) {
-        let o = !1;
-        for (const c of t) {
-          const l = `Derives_from,${i}`, u = this._completedReferences[c] || (this._completedReferences[c] = {});
-          u[l] && (o = !0), u[l] = !0;
-        }
-        if (!o)
-          for (const c of s)
-            c.derived_features.push(e);
-      } else {
-        let o = this._underConstructionOrphans[i];
-        o || (o = { Parent: [], Derives_from: [] }, this._underConstructionOrphans[i] = o), o.Derives_from.push(e);
-      }
-    }
-  }
-}
-function x(n) {
-  const e = [], r = new h({
-    featureCallback: (t) => e.push(t),
-    disableDerivesFromReferences: !0,
-    errorCallback: (t) => {
-      throw new Error(t);
-    }
-  });
-  for (const t of n.split(/\r?\n/))
-    r.addLine(t);
-  return r.finish(), e;
-}
-function w(n) {
-  const e = [], r = new h({
-    featureCallback: (t) => e.push(t),
-    disableDerivesFromReferences: !0,
-    errorCallback: (t) => {
-      throw new Error(t);
-    }
-  });
-  for (const t of n)
-    r.addLine(t);
-  return r.finish(), e;
-}
-function S(n) {
-  const e = [], r = new h({
-    featureCallback: (t) => e.push(t),
-    disableDerivesFromReferences: !0,
-    errorCallback: (t) => {
-      throw new Error(t);
-    }
-  });
-  for (const t of n) {
-    const i = d(t.fields);
-    t.lineHash !== void 0 && (i.attributes || (i.attributes = {}), i.attributes._lineHash = [String(t.lineHash)]), r.addParsedFeatureLine(i);
-  }
-  return r.finish(), e;
-}
-function E(n, e) {
-  const r = [], t = new h({
-    featureCallback: (s) => r.push(s),
-    disableDerivesFromReferences: !0,
-    errorCallback: (s) => {
-      throw new Error(s);
-    }
-  }), i = e ? d : R;
-  for (const s of n) {
-    const o = i(s.fields);
-    s.lineHash !== void 0 && (o.attributes || (o.attributes = {}), o.attributes._lineHash = [String(s.lineHash)]), t.addParsedFeatureLine(o);
-  }
-  return t.finish(), r;
-}
-export {
-  w as parseArraySync,
-  S as parseRecordsSync,
-  E as parseRecordsSyncFast,
-  x as parseStringSync
-};